James Fellows Yates
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a0ee82bf43
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Add motus/merge and biom support
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2022-07-12 11:39:26 +02:00 |
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James A. Fellows Yates
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8082c7d108
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Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
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2022-07-05 15:17:52 +02:00 |
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James A. Fellows Yates
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26e31c782d
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Merge branch 'dev' into motus
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2022-07-04 13:14:42 +02:00 |
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James Fellows Yates
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02c06b9f7b
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Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
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2022-06-30 18:33:11 +02:00 |
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James Fellows Yates
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27f174d17e
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Merge remote-tracking branch 'origin/dev' into malt-to-krona
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2022-06-30 12:01:33 +02:00 |
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James Fellows Yates
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0050f45345
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Add taxonomy directory param
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2022-06-30 11:43:52 +02:00 |
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6673ccf8d8
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Update channel assignment alignment in profiling subworkflow
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-06-28 09:00:43 -05:00 |
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4de43040a3
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Switch to using raw classifications for Kaiju2Krona
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2022-06-28 09:00:41 -05:00 |
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821dd844d8
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Add Kaiju profile conversion to visualization workflow
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2022-06-27 09:23:20 -05:00 |
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23fec89b06
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Add Krona chart creation for Centrifuge reports
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2022-06-27 08:52:29 -05:00 |
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a40a442178
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Create VISUALIZATION_KRONA workflow to create Krona charts
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2022-06-27 08:22:47 -05:00 |
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James Fellows Yates
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e0ad49ebc9
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Fix metadata manipulaton for malt
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2022-06-10 19:33:37 +02:00 |
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James A. Fellows Yates
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621b6a3d09
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Add comments about MALT id replacement and refactor for simplicity
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2022-06-10 11:27:51 +02:00 |
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James A. Fellows Yates
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ebdd5683b2
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Apply suggestions from code review
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2022-06-03 22:33:48 +02:00 |
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James Fellows Yates
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9462032d00
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Fix MALT save_alignemnts reads and some clean up
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2022-06-03 22:29:04 +02:00 |
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JIANHONG OU
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c8a59adbce
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remove the database auto-download for mOTUs.
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2022-06-03 14:13:58 -04:00 |
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James A. Fellows Yates
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96fecb2bfc
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Merge branch 'dev' into support-aligned-reads
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2022-06-03 13:48:54 +02:00 |
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James A. Fellows Yates
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53c4399052
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Merge branch 'dev' into motus
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2022-06-02 21:38:35 +02:00 |
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James A. Fellows Yates
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c9581b1796
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Merge branch 'dev' into support-aligned-reads
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2022-06-02 12:45:29 +02:00 |
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James Fellows Yates
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310ac6b450
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Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
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2022-05-31 13:05:52 +02:00 |
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JIANHONG OU
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4b3216c1cb
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filter fasta inputs for mOTUs;
fix the typo for nopreprocessing in nextflow.config.
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2022-05-24 08:42:18 -04:00 |
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JIANHONG OU
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68d0cc00fa
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add motus profile.
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2022-05-23 08:05:06 -04:00 |
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James Fellows Yates
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47a5ae0cff
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Add FASTP complexity option
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2022-05-07 06:09:05 +02:00 |
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James Fellows Yates
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87a1d80519
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Add working output for Kraken2/Centrifuge/DIAMOND
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2022-05-07 05:22:35 +02:00 |
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James A. Fellows Yates
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e7b54801ed
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Merge pull request #75 from nf-core/improve-error-message
Only create profiler input channels when profiler activated
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2022-05-06 11:51:33 +02:00 |
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ljmesi
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5e6be52fab
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Implement hostremoval
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2022-05-03 09:34:27 +02:00 |
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James Fellows Yates
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d5049a34e4
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Add missing close bracket
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2022-05-01 07:28:29 +02:00 |
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James Fellows Yates
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4094706421
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Only create profiler input channels when profiler activate
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2022-05-01 07:24:58 +02:00 |
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James Fellows Yates
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031cb45934
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Add initial longread QC filtering - requires filtlong module update
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2022-05-01 07:18:14 +02:00 |
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James Fellows Yates
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8126d16dee
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Add draft version of DIAMOND
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2022-04-29 21:59:42 +02:00 |
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sofstam
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d082d67bcb
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Add kaiju2table to taxprofiler
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2022-04-25 17:36:29 +02:00 |
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James A. Fellows Yates
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bc84afe80d
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Merge pull request #66 from nf-core/versions-fix
Fix version reporting
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2022-04-25 16:38:28 +02:00 |
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James Fellows Yates
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06b38f3699
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Fix crash, add missing versions
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2022-04-23 08:36:01 +02:00 |
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sofstam
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c00ca1c2b8
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Add centrifuge kreport in taxprofiler
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2022-04-22 15:24:10 +02:00 |
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Sofia Stamouli
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e71e7b86a2
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Merge pull request #53 from genomic-medicine-sweden/classification_kaiju
Add kaiju/kaiju in taxprofiler
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2022-04-20 10:57:00 +02:00 |
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Sofia Stamouli
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236141f065
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Resolve conflicts with dev
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2022-04-20 10:17:10 +02:00 |
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James A. Fellows Yates
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571495c812
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Merge pull request #60 from nf-core/fasta-filtering
Adds filtering out of FASTA for tools that don't support it
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2022-04-20 10:11:17 +02:00 |
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James Fellows Yates
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9fd94b1389
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Switch to string interpolation
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2022-04-20 09:25:54 +02:00 |
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James Fellows Yates
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60d232d62c
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Revert "Update subworkflows/local/profiling.nf"
This reverts commit b7d0557ee0 .
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2022-04-20 09:23:38 +02:00 |
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James A. Fellows Yates
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b7d0557ee0
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Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-20 09:15:45 +02:00 |
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James A. Fellows Yates
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87777a4289
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Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-19 12:54:57 +02:00 |
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James A. Fellows Yates
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ecaff371aa
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Update input_check.nf
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2022-04-18 07:35:19 +02:00 |
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James A. Fellows Yates
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9f634805e4
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Update subworkflows/local/profiling.nf
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2022-04-18 07:31:44 +02:00 |
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James A. Fellows Yates
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9c3c8f1f4e
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Merge branch 'dev' into fasta-filtering
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2022-04-18 07:31:14 +02:00 |
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James Fellows Yates
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6307a9cf43
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Typos
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2022-04-18 07:28:09 +02:00 |
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James Fellows Yates
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491c2d8949
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Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages."
This reverts commit 564474cafe .
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2022-04-18 07:26:15 +02:00 |
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James Fellows Yates
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564474cafe
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Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.
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2022-04-18 07:21:12 +02:00 |
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James Fellows Yates
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cc73cdd51d
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Add generation of taxon-table like output for MALT
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2022-04-16 07:42:30 +02:00 |
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James A. Fellows Yates
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6fecb3eeb7
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Merge pull request #54 from nf-core/dev
Get upstream changes
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2022-04-16 06:17:33 +02:00 |
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sofstam
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68ce5843a4
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Add kaiju in taxprofiler
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2022-04-13 18:51:56 +02:00 |
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